"This is an important step forward," Barroso said in a statement, welcoming the support which the Slovenian people gave to the agreement at the referendum.
"We now look forward to a final settlement of the dispute. Resolving this bilateral issue is an important signal for the region and the relations between Slovenia and Croatia," he said in the statement.
The border arbitration agreement won a narrow support at Sunday's referendum in Slovenia with 51.46 per cent of voters expressing their approval of the deal with Croatia and 48.52 per cent voting against it.
The results were published by the Slovenian election commission on late Sunday evening after 99.9 per cent of the ballots were processed. Those are incomplete results and final and complete results are expected on Tuesday.
Slovenian Foreign Minister Samuel Zbogar told the national television on Sunday evening that the referendum result was sending a positive message to the region.